“Clinician’s Probability Calculator” to Convert Pre-Test to Post-Test Probability of COVID-19, Based on Method Validation from Each Laboratory (original) (raw)

COVID-19 Testing – Impact of Prevalence, Sensitivity, and Specificity on Patient Risk and Cost

2020

Since the beginning of the year 2020, the global healthcare system has been challenged by the threat of the SARS-COV 2 virus. Molecular, antigen, and antibody testing are the mainstay to identify infected patients and fight the virus. Molecular and antigen tests that detect the presence of the virus are relevant in the acute phase only. Serological assays detect antibodies to the Sars-CoV-2 virus in the recovering and recovered phase. Each testing methodology has its advantages and disadvantages. To evaluate the test methods, sensitivity (percent positive agreement - PPA) and specificity (percent negative agreement – PNA) are the most common metrics utilized, followed by the positive and negative predictive value (PPV and NPV), the probability that a positive or negative test result represents a true positive or negative patient. In this paper, we illustrate how patient risk and clinical costs are driven by false-positive and false-negative results. We demonstrate the value of repor...

Clinical Prediction Tool to Assess the Likelihood of a Positive SARS-Cov-2 (COVID-19) Polymerase Chain Reaction Test in Patients with Flu-like Symptoms

Western Journal of Emergency Medicine

Introduction: The clinical presentation of coronavirus disease 2019 (COVID-19) overlaps with many other common cold and influenza viruses. Identifying patients with a higher probability of infection becomes crucial in settings with limited access to testing. We developed a prediction instrument to assess the likelihood of a positive polymerase chain reaction (PCR) test, based solely on clinical variables that can be determined within the time frame of an emergency department (ED) patient encounter. Methods: We derived and prospectively validated a model to predict SARS-CoV-2 PCR positivity in patients visiting the ED with symptoms consistent with the disease. Results: Our model was based on 617 ED visits. In the derivation cohort, the median age was 36 years, 43% were men, and 9% had a positive result. The median time to testing from the onset of initial symptoms was four days (interquartile range [IQR]: 2-5 days, range 0-23 days), and 91% of all patients were discharged home. The final model based on a multivariable logistic regression included a history of close contact (adjusted odds ratio [AOR] 2.47, 95% confidence interval [CI],

Predicting patients with false negative SARS-CoV-2 testing at hospital admission: A retrospective multi-center study

2020

ImportanceFalse negative SARS-CoV-2 tests can lead to spread of infection in the inpatient setting to other patients and healthcare workers. However, the population of patients with COVID who are admitted with false negative testing is unstudied.ObjectiveTo characterize and develop a model to predict true SARS-CoV-2 infection among patients who initially test negative for COVID by PCR.DesignRetrospective cohort study.SettingFive hospitals within the Yale New Haven Health System between 3/10/2020 and 9/1/2020. Participants: Adult patients who received diagnostic testing for SARS-CoV-2 virus within the first 96 hours of hospitalization.ExposureWe developed a logistic regression model from readily available electronic health record data to predict SARS-CoV-2 positivity in patients who were positive for COVID and those who were negative and never retested.Main Outcomes and MeasuresThis model was applied to patients testing negative for SARS-CoV-2 who were retested within the first 96 ho...

Disease Prevalence Matters: Challenge for SARS-CoV-2 Testing

Antibodies

While sensitivity and specificity are important characteristics for any diagnostic test, the influence of prevalence is equally, if not more, important when such tests are used in community screening. We review the concepts of positive/negative predictive values (PPV/NPV) and how disease prevalence affects false positive/negative rates. In low-prevalence situations, the PPV decreases drastically. We demonstrate how using two tests in an orthogonal fashion can be especially beneficial in low-prevalence settings and greatly improve the PPV of the diagnostic test results.

Diagnostic Yield of Screening for SARS-CoV-2 among Patients Admitted for Alternate Diagnoses

2021

ObjectivesTo determine the diagnostic yield of screening patients for SARS-CoV-2 who were admitted with a diagnosis unrelated to COVID-19, and identify risk factors for positive tests.DesignCohort from the Canadian COVID-19 Emergency Department Rapid Response Network (CCEDRRN) registrySetting30 acute care hospitals across CanadaParticipantsPatients hospitalized for non-COVID-19 related diagnoses who were tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between March 1, and December 29, 2020Main outcomePositive nucleic acid amplification test (NAAT) for SARS-CoV-2Outcome measureDiagnostic yieldResultsWe enrolled 15,690 consecutive eligible adults who were admitted to hospital without clinically suspected COVID-19. Among these patients, 122 tested positive for COVID-19, resulting in a diagnostic yield of 0.8% (95% CI 0.64% – 0.92%). Factors associated with a positive test included presence of a fever, being a healthcare worker, having a positive household contac...

Pre-test probability for SARS-Cov-2-related Infection Score: the PARIS score

2020

BackgroundDiagnostic tests for SARS-CoV-2 infection (mostly RT-PCR and Computed Tomography) are not widely available in numerous countries, expensive and with imperfect performanceMethodsThis multicenter retrospective study aimed to determine a pre-test probability score for SARS-CoV-2 infection based on clinical and biological variables. Patients were recruited from emergency and infectious disease departments and were divided into a training and a validation cohort. Demographic characteristics, clinical symptoms, and results of blood tests (complete white blood cell count, serum electrolytes and CRP) were collected. The pre-test probability score was derived from univariate analyses between patients and controls, followed by multivariate binary logistic analysis to determine the independent variables associated with SARS-CoV-2 infection. Points were assigned to each variable to create the PARIS score. ROC curve analysis determined the area under the curve (AUC).FindingsOne hundred...

Sensitivity, Specificity and Predictive Values of Molecular and Serological Tests for COVID-19: A Longitudinal Study in Emergency Room

Diagnostics

Background: We assessed the sensitivity, specificity and positive and negative predictive value (PPV and NPV) of molecular and serological tests for the diagnosis of SARS-CoV-2 infection. Methods: A total of 346 patients were enrolled in the emergency room. We evaluated three Reverse Transcriptase-real time PCRs (RT-PCRs) including six different gene targets, five serologic rapid diagnostic tests (RDT) and one ELISA. The final classification of infected/non-infected patients was performed using Latent Class Analysis combined with clinical re-assessment of incongruous cases. Results: Out of these, 24.6% of patients were classified as infected. The molecular test RQ-SARS-nCoV-2 showed the highest performance with 91.8% sensitivity, 100% specificity, 100.0% PPV and 97.4% NPV respectively. Considering the single gene targets, S and RdRp of RQ-SARS-nCoV-2 had the highest sensitivity (94.1%). The in-house RdRp presented the lowest sensitivity (62.4%). The specificity ranged from 99.2% for...

Characteristics of SARS-CoV-2 testing for rapid diagnosis of COVID-19 during the initial stages of a global pandemic

PLoS ONE, 2021

Accurate SARS-CoV-2 diagnosis is essential to guide prevention and control of COVID-19. Here we examine SARS-CoV-2 molecular-based test performance characteristics and summarize case-level data related to COVID-19 diagnosis. From January 11 through April 22, 2020, Public Health Ontario conducted SARS-CoV-2 testing of 86,942 specimens collected from 80,354 individuals, primarily using real-time reverse-transcription polymerase chain reaction (rRT-PCR) methods. We analyzed test results across specimen types and for individuals with multiple same-day and multi-day collected specimens. Nasopharyngeal compared to throat swabs had a higher positivity (8.8% vs. 4.8%) and an adjusted estimate 2.9 Ct lower (SE = 0.5, p<0.001). Same-day specimens showed high concordance (98.8%), and the median Ct of multi-day specimens increased over time. Symptomatic cases had rRT-PCR results with an adjusted estimate 3.0 Ct (SE = 0.5, p<0.001) lower than asymptomatic/pre-symptomatic cases. Overall tes...